Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

BACKGROUND: Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. RESULTS: Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. CONCLUSIONS: Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens

Muon Capture on the Proton and Deuteron

By measuring the lifetime of the negative muon in pure protium (hydrogen-1), the MuCap experiment determines the rate of muon capture on the proton, from which the proton's pseudoscalar coupling g_p may be inferred. A precision of 15% for g_p has been published; this is a step along the way to a goal of 7%. This coupling can be calculated precisely from heavy baryon chiral perturbation theory and therefore permits a test of QCD's chiral symmetry. Meanwhile, the MuSun experiment is in its final design stage; it will measure the rate of muon capture on the deuteron using a similar technique. This process can be related through pionless effective field theory and chiral perturbation theory to other two-nucleon reactions of astrophysical interest, including proton-proton fusion and deuteron breakup.Comment: Submitted to the proceedings of the 2007 Advanced Studies Institute on Symmetries and Spin (SPIN-Praha-2007

Factorizing the hard and soft spectator scattering contributions for the nucleon form factor F_1 at large Q^2

We investigate the soft spectator scattering contribution for the FF $F_{1}$. We focus our attention on factorization of the hard-collinear scale $\sim Q\Lambda$ corresponding to transition from SCET-I to SCET-II. We compute the leading order jet functions and find that the convolution integrals over the soft fractions are logarithmically divergent. This divergency is the consequence of the boost invariance and does not depend on the model of the soft correlation function describing the soft spectator quarks. Using as example a two-loop diagram we demonstrated that such a divergency corresponds to the overlap of the soft and collinear regions. As a result one obtains large rapidity logarithm which must be included in the correct factorization formalism. We conclude that a consistent description of the factorization for $F_{1}$ implies the end-point collinear divergencies in the hard and soft spectator contributions, i.e. convolution integrals with respect to collinear fractions are not well-defined. Such scenario can only be realized when the twist-3 nucleon distribution amplitude has specific end-point behavior which differs from one expected from the evolution of the nucleon distribution amplitude. Such behavior leads to the violation of the collinear factorization for the hard spectator scattering contribution. We suggest that the soft spectator scattering and chiral symmetry breaking provide the mechanism responsible for the violation of collinear factorization in case of form factor $F_{1}$.Comment: 25 pages, 6 figures, text is improved, few typos corrected, one figure added, statement about end-point behavior of the nucleon DA is formulated more accuratel

Dynamic splitting of a Bose-Einstein Condensate

We study the dynamic process of splitting a condensate by raising a potential barrier in the center of a harmonic trap. We use a two-mode model to describe the phase coherence between the two halves of the condensate. Furthermore, we explicitly consider the spatial dependence of the mode funtions, which varies depending on the potential barrier. This allows to get the tunneling coupling between the two wells and the on-site energy as a function of the barrier height. Moreover we can get some insight on the collective modes which are excited by raising the barrier. We describe the internal and external degrees of freedom by variational ansatz. We distinguish the possible regimes as a function of the characteristic parameters of the problem and identify the adiabaticity conditions.Comment: 17 pages, 8 figure

Magnetic fileds of coalescing neutron stars and the luminosity function of short gamma-ray burst

Coalescing neutron star binaries are believed to be the most reliable sources for ground-based detectors of gravitational waves and likely progenitors of short gamma-ray bursts. In the process of coalescence, magnetic fields of neutron stars can induce interesting observational manifestations and affect the form of gravitational wave signal. In this papaer we use the population synthesis method to model the expected distribution of neutron star magnetic fields during the coalescence under different assumptions on the initial parameters of neutron stars and their magnetic field evolution. We discuss possible elecotrmagnetic phenomena preceding the coalescence of magnetized neutron star binaries and the effect of magnetic field on the gravitational wave signal. We find that a log-normal (Gaussian in logarithms) distribution of the initial magnetic fields of neutron stars, which agrees with observed properties of radio pulsars, produces the distribution of the magnetic field energy during the coalescence that adequately describes the observed luminosity function of short gamma-ray bursts under different assumptions on the field evolution and initial parameters of neutron stars. This agreement lends further support to the model of coalescing neutron star binaries as progenitors of gamma-ray bursts.Comment: v.2, LATEX, 25 pages, inc. 7 ps figures, Astron. Lett., in press. Typos corrected, reference adde

Search for the glueball candidates f0(1500) and fJ(1710) in gamma gamma collisions

Data taken with the ALEPH detector at LEP1 have been used to search for gamma gamma production of the glueball candidates f0(1500) and fJ(1710) via their decay to pi+pi-. No signal is observed and upper limits to the product of gamma gamma width and pi+pi- branching ratio of the f0(1500) and the fJ(1710) have been measured to be Gamma_(gamma gamma -> f0(1500)). BR(f0(1500)->pi+pi-) < 0.31 keV and Gamma_(gamma gamma -> fJ(1710)). BR(fJ(1710)->pi+pi-) < 0.55 keV at 95% confidence level.Comment: 10 pages, 3 figure

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters